EESSI
EESSI repository
EESSI, short for the European Environment for Scientific Software Installations, is a collaborated project between different European partners in HPC community to build a common stack of scientific software installations for HPC systems and beyond. Through the EESSI project, a shared stack of scientific software installations is distributed via CVMFS.
The official website of EESSI can be found in EESSI website. To get an overview of all the available software in EESSI per specific CPU target, please check EESSI available software. Below we give instructions on how to make use of EESSI repository in Spider.
Basic usage
To access the EESSI software stack, first set up the EESSI environment by running the command:
source /cvmfs/software.eessi.io/versions/2023.06/init/bash
You should be able to see the following output
Found EESSI repo @ /cvmfs/software.eessi.io/versions/2023.06!
archdetect says x86_64/amd/zen2
Using x86_64/amd/zen2 as software subdirectory.
Found Lmod configuration file at /cvmfs/software.eessi.io/versions/2023.06/software/linux/x86_64/amd/zen2/.lmod/lmodrc.lua
Found Lmod SitePackage.lua file at /cvmfs/software.eessi.io/versions/2023.06/software/linux/x86_64/amd/zen2/.lmod/SitePackage.lua
Using /cvmfs/software.eessi.io/versions/2023.06/software/linux/x86_64/amd/zen2/modules/all as the directory to be added to MODULEPATH.
Using /cvmfs/software.eessi.io/host_injections/2023.06/software/linux/x86_64/amd/zen2/modules/all as the site extension directory to be added to MODULEPATH.
Initializing Lmod...
Prepending /cvmfs/software.eessi.io/versions/2023.06/software/linux/x86_64/amd/zen2/modules/all to $MODULEPATH...
Prepending site path /cvmfs/software.eessi.io/host_injections/2023.06/software/linux/x86_64/amd/zen2/modules/all to $MODULEPATH...
Environment set up to use EESSI (2023.06), have fun!
{EESSI 2023.06} [xxxxx@ui-01 ~]$
The last line is the shell prompt where you can run your bash commands.
To check the available software modules, simply run command
module avail
To find a specific software module, run command
module spider python
You can directly load the modules that you need. For example, to load Python module
module load Python/3.10.8-GCCcore-12.2.0
Using EESSI software in a job script
You can also use the EESSI software stack in a job script in Spider by inclduing the source command and loading the modules. Below is an example job script:
#!/bin/bash
#SBATCH -N 1
#SBATCH -t 10:00
#SBATCH -c 1
#SBTACH -p normal
# source the EESSI environment
source /cvmfs/software.eessi.io/versions/2023.06/init/bash
# load the modules in EESSI
module load matplotlib/3.7.0-gfbf-2022b
module load Python/3.10.8-GCCcore-12.2.0
# confim that EESSI repository is used
echo "I am running on " $HOSTNAME
var=$(which python)
echo "I am using python in " $var
# run the python work
python /home/$USER/draw_a_plot.py
The draw_a_plot.py can be, for example:
import numpy as np
import matplotlib.pyplot as plt
x = np.arange(0, 5, 0.1)
y = np.sin(x)
plt.plot(x, y)
plt.savefig("output.jpg")
To view the result jpg and job output in your terminal, run commands
display output.jpg
cat slurm-job-id.out